NAME
ribbon - Raster3D molecular graphics package ribbon-drawer
SYNOPSIS
"ribbon" [-h] [-d[0123456]] pdbfile
or
"ribbon" [-h] -d[0123456] - (to take PDB records from stdin)
Ribbon reads a PDB coordinate file and produces a file on stdout
containing Raster3D descriptor records for a ribbon representation
constructed from a triangular mesh. The file produced by ribbon may be
fed directly to render or it may be combined with descriptor files
produced by other Raster3D utilities.
EXAMPLES
To describe a the entire protein chain as a single ribbon colored
smoothly from blue at the N-terminus to red at the C-terminus:
ribbon -d2 protein.pdb | render > chain_picture.avs
To color a multi-chain protein with specified colors for each chain:
cat chaincolors.pdb protein.pdb | ribbon -d5 - > chains.r3d
OPTIONS
-h
Suppress header records in output. By default ribbon will produce an
output file which starts with header records containing a default set
of scaling and processing options. The -h flag will suppress these
header records so that the output file contains only triangle
descriptors. This option is useful for producing files which describe
only part of a scene, and which are to be later combined with
descriptor files produced by other programs.
-d[0123456]
By default ribbon requires interactive input to select ribbon
parameters and coloring information. Five default coloring schemes are
implemented, however, and these may be selected as a command line
option to bypass any interactive input.
-d or -d0 same as -d2 below
-d1 solid color ribbon (defaults to blue)
-d2 shade from blue at N-terminus to red at C-terminus
-d3 one surface of ribbon is blue, other surface is grey
-d4 shade front surface from blue to red, back surface is grey
-d5 color separate chains using successive color cards
from input stream. Note that pattern matching on the color records
is _not_ done; colors are simply taken sequentially as new chains
are encountered.
-d6 Color by nearest CA atom as taken from the COLOUR
records at the head of the input file
DESCRIPTION
The input to ribbon consists of a single text file containing colour
information [optional] and atomic coordinates in PDB data bank format.
Only CA and carbonyl O atom records are required; all other input atoms
are ignored. Ribbon parameters and colouring specified interactively
when the program is run. Keyboard interaction may be bypassed by
selecting one of the default colouring schemes using the -d flag. A
triangular mesh ribbon is output as Raster3D descriptor records. By
default the output file contains a set of header records as required by
the render program. The header is constructed to include a TMAT matrix
corresponding to the transformation matrix contained in file
setup.matrix (if it exists), or to the Eulerian angles contained in
file setup.angles (if it exists).
Ribbon produces a continuous smooth trace of the protein backbone. For
more complicated representations of protein secondary structure it is
better to use a different program, e.g. MOLSCRIPT, rather than ribbon.
ENVIRONMENT
The files setup.matrix and setup.angles, if they exist, affect the
header records produced by ribbon.
SOURCE
anonymous ftp site:
ftp.bmsc.washington.edu
web URL:
http://www.bmsc.washington.edu/raster3d/raster3d.html
contact:
Ethan A Merritt
University of Washington, Seattle WA 98195
merritt@u.washington.edu
SEE ALSO
MOLSCRIPT(l), render(l), rods(l), balls(l)
AUTHORS
Original ribbon code written by Phil Evans for the CCP4 version of
FRODO. Modification to describe solid ribbons as triangular mesh for
Phong shading in Raster3D package by Ethan A Merritt.